Starting phenix.real_space_refine on Sun Apr 5 01:28:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21cq_67575/04_2026/21cq_67575.cif Found real_map, /net/cci-nas-00/data/ceres_data/21cq_67575/04_2026/21cq_67575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21cq_67575/04_2026/21cq_67575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21cq_67575/04_2026/21cq_67575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21cq_67575/04_2026/21cq_67575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21cq_67575/04_2026/21cq_67575.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 54 5.49 5 S 29 5.16 5 C 4144 2.51 5 N 1146 2.21 5 O 1408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6783 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1144 Classifications: {'RNA': 54} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 26, 'rna3p_pyr': 27} Link IDs: {'rna2p': 1, 'rna3p': 52} Chain breaks: 1 Chain: "D" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5637 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 48, 'TRANS': 651} Chain breaks: 4 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.50, per 1000 atoms: 0.22 Number of scatterers: 6783 At special positions: 0 Unit cell: (63.06, 71.468, 131.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 29 16.00 P 54 15.00 O 1408 8.00 N 1146 7.00 C 4144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 221.1 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 49.6% alpha, 2.4% beta 19 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'D' and resid 781 through 785 removed outlier: 4.399A pdb=" N LEU D 785 " --> pdb=" O PRO D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 857 Processing helix chain 'D' and resid 893 through 903 removed outlier: 3.948A pdb=" N MET D 897 " --> pdb=" O ASP D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 914 removed outlier: 3.553A pdb=" N TYR D 914 " --> pdb=" O SER D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 929 removed outlier: 4.020A pdb=" N GLN D 928 " --> pdb=" O LEU D 924 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 976 Processing helix chain 'D' and resid 997 through 1001 Processing helix chain 'D' and resid 1018 through 1028 Processing helix chain 'D' and resid 1034 through 1039 Processing helix chain 'D' and resid 1044 through 1052 removed outlier: 4.594A pdb=" N LYS D1050 " --> pdb=" O SER D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1053 through 1074 Processing helix chain 'D' and resid 1293 through 1302 removed outlier: 3.978A pdb=" N ALA D1300 " --> pdb=" O LEU D1296 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D1302 " --> pdb=" O LEU D1298 " (cutoff:3.500A) Processing helix chain 'D' and resid 1303 through 1307 Processing helix chain 'D' and resid 1313 through 1335 Processing helix chain 'D' and resid 1341 through 1354 Processing helix chain 'D' and resid 1356 through 1361 Processing helix chain 'D' and resid 1555 through 1574 removed outlier: 3.993A pdb=" N ALA D1560 " --> pdb=" O ASP D1556 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP D1561 " --> pdb=" O LYS D1557 " (cutoff:3.500A) Processing helix chain 'D' and resid 1575 through 1586 removed outlier: 3.713A pdb=" N ALA D1579 " --> pdb=" O GLY D1575 " (cutoff:3.500A) Processing helix chain 'D' and resid 1660 through 1662 No H-bonds generated for 'chain 'D' and resid 1660 through 1662' Processing helix chain 'D' and resid 1663 through 1674 removed outlier: 3.621A pdb=" N GLU D1667 " --> pdb=" O ILE D1663 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN D1668 " --> pdb=" O SER D1664 " (cutoff:3.500A) Processing helix chain 'D' and resid 1679 through 1687 removed outlier: 3.717A pdb=" N LEU D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) Processing helix chain 'D' and resid 1701 through 1723 Processing helix chain 'D' and resid 1728 through 1741 Processing helix chain 'D' and resid 1741 through 1752 Processing helix chain 'D' and resid 1766 through 1775 removed outlier: 3.870A pdb=" N PHE D1772 " --> pdb=" O VAL D1768 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D1773 " --> pdb=" O ILE D1769 " (cutoff:3.500A) Processing helix chain 'D' and resid 1805 through 1823 Processing helix chain 'D' and resid 1826 through 1835 Processing helix chain 'D' and resid 1838 through 1846 Processing helix chain 'D' and resid 1852 through 1861 removed outlier: 3.593A pdb=" N LEU D1857 " --> pdb=" O PRO D1853 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU D1858 " --> pdb=" O VAL D1854 " (cutoff:3.500A) Processing helix chain 'D' and resid 1896 through 1912 removed outlier: 3.544A pdb=" N ALA D1900 " --> pdb=" O SER D1896 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 803 through 805 Processing sheet with id=AA2, first strand: chain 'D' and resid 819 through 820 Processing sheet with id=AA3, first strand: chain 'D' and resid 881 through 883 Processing sheet with id=AA4, first strand: chain 'D' and resid 931 through 932 227 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1787 1.34 - 1.45: 1509 1.45 - 1.57: 3608 1.57 - 1.69: 107 1.69 - 1.81: 42 Bond restraints: 7053 Sorted by residual: bond pdb=" N VAL D1849 " pdb=" CA VAL D1849 " ideal model delta sigma weight residual 1.460 1.495 -0.035 9.30e-03 1.16e+04 1.44e+01 bond pdb=" N VAL D1854 " pdb=" CA VAL D1854 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.06e+00 bond pdb=" N SER D1852 " pdb=" CA SER D1852 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.13e-02 7.83e+03 7.59e+00 bond pdb=" N ASN D1848 " pdb=" CA ASN D1848 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.31e-02 5.83e+03 6.10e+00 bond pdb=" N ALA D1847 " pdb=" CA ALA D1847 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.18e-02 7.18e+03 5.70e+00 ... (remaining 7048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 9598 3.12 - 6.23: 198 6.23 - 9.35: 16 9.35 - 12.47: 1 12.47 - 15.58: 1 Bond angle restraints: 9814 Sorted by residual: angle pdb=" CB PRO D 817 " pdb=" CG PRO D 817 " pdb=" CD PRO D 817 " ideal model delta sigma weight residual 106.10 90.52 15.58 3.20e+00 9.77e-02 2.37e+01 angle pdb=" O3' C R 61 " pdb=" P U R 62 " pdb=" O5' U R 62 " ideal model delta sigma weight residual 104.00 110.99 -6.99 1.50e+00 4.44e-01 2.17e+01 angle pdb=" O4' A R 43 " pdb=" C1' A R 43 " pdb=" C2' A R 43 " ideal model delta sigma weight residual 107.60 103.27 4.33 1.00e+00 1.00e+00 1.88e+01 angle pdb=" C4' G R 1 " pdb=" C3' G R 1 " pdb=" O3' G R 1 " ideal model delta sigma weight residual 113.00 106.93 6.07 1.50e+00 4.44e-01 1.64e+01 angle pdb=" C3' U R 62 " pdb=" C2' U R 62 " pdb=" C1' U R 62 " ideal model delta sigma weight residual 101.30 105.28 -3.98 1.00e+00 1.00e+00 1.58e+01 ... (remaining 9809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.93: 3996 29.93 - 59.85: 285 59.85 - 89.78: 57 89.78 - 119.70: 6 119.70 - 149.63: 1 Dihedral angle restraints: 4345 sinusoidal: 2271 harmonic: 2074 Sorted by residual: dihedral pdb=" O4' U R 62 " pdb=" C4' U R 62 " pdb=" C3' U R 62 " pdb=" C2' U R 62 " ideal model delta sinusoidal sigma weight residual -35.00 20.30 -55.30 1 8.00e+00 1.56e-02 6.46e+01 dihedral pdb=" C5' U R 62 " pdb=" C4' U R 62 " pdb=" C3' U R 62 " pdb=" O3' U R 62 " ideal model delta sinusoidal sigma weight residual 82.00 136.26 -54.26 1 8.00e+00 1.56e-02 6.24e+01 dihedral pdb=" O4' U R 63 " pdb=" C1' U R 63 " pdb=" N1 U R 63 " pdb=" C2 U R 63 " ideal model delta sinusoidal sigma weight residual 232.00 82.37 149.63 1 1.70e+01 3.46e-03 6.19e+01 ... (remaining 4342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1046 0.113 - 0.227: 63 0.227 - 0.340: 2 0.340 - 0.454: 8 0.454 - 0.567: 19 Chirality restraints: 1138 Sorted by residual: chirality pdb=" P G R 1 " pdb=" OP1 G R 1 " pdb=" OP2 G R 1 " pdb=" O5' G R 1 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" P U R 18 " pdb=" OP1 U R 18 " pdb=" OP2 U R 18 " pdb=" O5' U R 18 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" P U R 62 " pdb=" OP1 U R 62 " pdb=" OP2 U R 62 " pdb=" O5' U R 62 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 1135 not shown) Planarity restraints: 1053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D1839 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO D1840 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D1840 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D1840 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D1804 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO D1805 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D1805 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D1805 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 749 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO D 750 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 750 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 750 " -0.030 5.00e-02 4.00e+02 ... (remaining 1050 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 4 2.10 - 2.80: 1801 2.80 - 3.50: 10383 3.50 - 4.20: 18132 4.20 - 4.90: 29605 Nonbonded interactions: 59925 Sorted by model distance: nonbonded pdb=" OP1 A R 43 " pdb="CA CA R2001 " model vdw 1.398 2.510 nonbonded pdb=" O LEU D1684 " pdb=" OG1 THR D1688 " model vdw 2.018 3.040 nonbonded pdb=" OG SER D1823 " pdb=" OG SER D1826 " model vdw 2.085 3.040 nonbonded pdb=" O SER D1348 " pdb=" OG SER D1352 " model vdw 2.091 3.040 nonbonded pdb=" OG SER D1826 " pdb=" OG1 THR D1829 " model vdw 2.102 3.040 ... (remaining 59920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 7053 Z= 0.311 Angle : 0.983 15.583 9814 Z= 0.510 Chirality : 0.091 0.567 1138 Planarity : 0.006 0.060 1053 Dihedral : 20.087 149.630 3005 Min Nonbonded Distance : 1.398 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.96 % Allowed : 23.68 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.32), residues: 690 helix: -0.02 (0.30), residues: 277 sheet: -3.37 (0.87), residues: 25 loop : -1.72 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1314 TYR 0.025 0.002 TYR D 971 PHE 0.033 0.002 PHE D1758 TRP 0.006 0.002 TRP D1380 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 7053) covalent geometry : angle 0.98343 ( 9814) hydrogen bonds : bond 0.16308 ( 272) hydrogen bonds : angle 7.12308 ( 730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.4271 (OUTLIER) cc_final: 0.3665 (mtp180) REVERT: D 971 TYR cc_start: 0.2119 (OUTLIER) cc_final: 0.0038 (p90) REVERT: D 1299 GLN cc_start: 0.5597 (tp-100) cc_final: 0.5345 (mm110) REVERT: D 1358 ARG cc_start: 0.3630 (tmm160) cc_final: 0.2808 (tmm160) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.1210 time to fit residues: 13.4668 Evaluate side-chains 86 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 944 ARG Chi-restraints excluded: chain D residue 971 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 8.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1695 ASN D1727 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.176621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.162806 restraints weight = 17728.614| |-----------------------------------------------------------------------------| r_work (start): 0.4758 rms_B_bonded: 2.97 r_work: 0.4647 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 7053 Z= 0.183 Angle : 0.772 8.835 9814 Z= 0.388 Chirality : 0.045 0.358 1138 Planarity : 0.006 0.064 1053 Dihedral : 18.620 154.609 1609 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.48 % Allowed : 22.24 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.31), residues: 690 helix: -0.00 (0.29), residues: 287 sheet: -3.24 (0.87), residues: 25 loop : -1.78 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 859 TYR 0.031 0.002 TYR D 976 PHE 0.023 0.002 PHE D1332 TRP 0.041 0.003 TRP D1048 HIS 0.006 0.002 HIS D 943 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 7053) covalent geometry : angle 0.77206 ( 9814) hydrogen bonds : bond 0.06396 ( 272) hydrogen bonds : angle 5.98938 ( 730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 87 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 971 TYR cc_start: 0.2067 (OUTLIER) cc_final: -0.0545 (p90) REVERT: D 1320 ASP cc_start: 0.4554 (t0) cc_final: 0.4325 (t0) REVERT: D 1722 GLU cc_start: 0.4895 (OUTLIER) cc_final: 0.4587 (mp0) REVERT: D 1831 TRP cc_start: 0.5673 (t-100) cc_final: 0.5213 (t-100) outliers start: 28 outliers final: 11 residues processed: 105 average time/residue: 0.1110 time to fit residues: 14.7821 Evaluate side-chains 86 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1705 GLU Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.0000 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1668 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4917 r_free = 0.4917 target = 0.173994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.159760 restraints weight = 17684.232| |-----------------------------------------------------------------------------| r_work (start): 0.4712 rms_B_bonded: 3.05 r_work: 0.4601 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7053 Z= 0.184 Angle : 0.727 8.390 9814 Z= 0.373 Chirality : 0.043 0.207 1138 Planarity : 0.006 0.054 1053 Dihedral : 18.435 161.086 1599 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.76 % Allowed : 22.72 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.31), residues: 690 helix: 0.01 (0.29), residues: 287 sheet: -3.19 (0.88), residues: 25 loop : -1.75 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 996 TYR 0.029 0.002 TYR D 976 PHE 0.024 0.002 PHE D1332 TRP 0.059 0.004 TRP D1048 HIS 0.007 0.002 HIS D 856 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 7053) covalent geometry : angle 0.72659 ( 9814) hydrogen bonds : bond 0.05993 ( 272) hydrogen bonds : angle 5.91366 ( 730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.4388 (OUTLIER) cc_final: 0.4045 (mtm180) REVERT: D 936 TYR cc_start: 0.4594 (OUTLIER) cc_final: 0.4390 (t80) REVERT: D 971 TYR cc_start: 0.2116 (OUTLIER) cc_final: -0.0934 (p90) REVERT: D 1320 ASP cc_start: 0.4892 (t0) cc_final: 0.4659 (t0) REVERT: D 1362 LYS cc_start: 0.4209 (pttp) cc_final: 0.3999 (tmtt) REVERT: D 1831 TRP cc_start: 0.5779 (t-100) cc_final: 0.5407 (t-100) outliers start: 36 outliers final: 20 residues processed: 107 average time/residue: 0.0987 time to fit residues: 13.6246 Evaluate side-chains 103 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1352 SER Chi-restraints excluded: chain D residue 1365 LEU Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1662 LEU Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1705 GLU Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1890 PHE Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 747 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.173665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.159238 restraints weight = 17669.033| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 3.08 r_work: 0.4588 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 7053 Z= 0.179 Angle : 0.722 8.784 9814 Z= 0.367 Chirality : 0.045 0.353 1138 Planarity : 0.006 0.045 1053 Dihedral : 18.354 163.122 1599 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.96 % Allowed : 23.52 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.31), residues: 690 helix: -0.01 (0.29), residues: 283 sheet: -3.23 (0.84), residues: 25 loop : -1.74 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 944 TYR 0.024 0.003 TYR D1701 PHE 0.022 0.002 PHE D1332 TRP 0.044 0.004 TRP D1048 HIS 0.006 0.001 HIS D 856 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 7053) covalent geometry : angle 0.72239 ( 9814) hydrogen bonds : bond 0.05909 ( 272) hydrogen bonds : angle 5.90542 ( 730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 770 LEU cc_start: 0.2473 (OUTLIER) cc_final: 0.2181 (tt) REVERT: D 800 ARG cc_start: 0.4126 (OUTLIER) cc_final: 0.3654 (mtm180) REVERT: D 830 GLU cc_start: 0.6132 (mp0) cc_final: 0.5777 (mp0) REVERT: D 857 ILE cc_start: 0.3563 (mt) cc_final: 0.3218 (mt) REVERT: D 936 TYR cc_start: 0.4690 (OUTLIER) cc_final: 0.4257 (t80) REVERT: D 971 TYR cc_start: 0.2264 (OUTLIER) cc_final: -0.0992 (p90) REVERT: D 1048 TRP cc_start: 0.2972 (t-100) cc_final: 0.2682 (t-100) REVERT: D 1320 ASP cc_start: 0.5066 (t0) cc_final: 0.4809 (t0) REVERT: D 1831 TRP cc_start: 0.5943 (t-100) cc_final: 0.5587 (t-100) outliers start: 31 outliers final: 15 residues processed: 102 average time/residue: 0.1187 time to fit residues: 15.1852 Evaluate side-chains 104 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 913 LYS Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1365 LEU Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1821 MET Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.171398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.155855 restraints weight = 16886.953| |-----------------------------------------------------------------------------| r_work (start): 0.4660 rms_B_bonded: 3.22 r_work: 0.4541 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5608 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 7053 Z= 0.194 Angle : 0.741 7.092 9814 Z= 0.377 Chirality : 0.044 0.174 1138 Planarity : 0.006 0.046 1053 Dihedral : 18.395 163.979 1599 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.44 % Allowed : 24.64 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.31), residues: 690 helix: -0.23 (0.29), residues: 281 sheet: -3.34 (0.80), residues: 25 loop : -1.79 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 996 TYR 0.027 0.002 TYR D1701 PHE 0.024 0.002 PHE D1332 TRP 0.019 0.003 TRP D1048 HIS 0.006 0.001 HIS D 856 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 7053) covalent geometry : angle 0.74060 ( 9814) hydrogen bonds : bond 0.06065 ( 272) hydrogen bonds : angle 6.02625 ( 730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 830 GLU cc_start: 0.6353 (mp0) cc_final: 0.5988 (mp0) REVERT: D 936 TYR cc_start: 0.4715 (OUTLIER) cc_final: 0.4075 (t80) REVERT: D 971 TYR cc_start: 0.2640 (OUTLIER) cc_final: -0.1229 (p90) REVERT: D 1320 ASP cc_start: 0.5162 (t0) cc_final: 0.4865 (t0) REVERT: D 1831 TRP cc_start: 0.5908 (t-100) cc_final: 0.5531 (t-100) REVERT: D 1909 LEU cc_start: 0.6689 (mm) cc_final: 0.6402 (tp) outliers start: 34 outliers final: 20 residues processed: 112 average time/residue: 0.1107 time to fit residues: 15.7659 Evaluate side-chains 106 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 913 LYS Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1357 TYR Chi-restraints excluded: chain D residue 1365 LEU Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1662 LEU Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 28 optimal weight: 0.0010 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.4224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.173654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.159110 restraints weight = 17777.358| |-----------------------------------------------------------------------------| r_work (start): 0.4703 rms_B_bonded: 3.10 r_work: 0.4588 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7053 Z= 0.157 Angle : 0.708 6.575 9814 Z= 0.362 Chirality : 0.042 0.172 1138 Planarity : 0.006 0.076 1053 Dihedral : 18.347 163.890 1599 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.16 % Allowed : 26.24 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.31), residues: 690 helix: -0.09 (0.29), residues: 283 sheet: -3.73 (0.76), residues: 25 loop : -1.79 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 944 TYR 0.021 0.002 TYR D1701 PHE 0.021 0.002 PHE D1332 TRP 0.027 0.003 TRP D1048 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7053) covalent geometry : angle 0.70764 ( 9814) hydrogen bonds : bond 0.05920 ( 272) hydrogen bonds : angle 5.84881 ( 730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.3787 (OUTLIER) cc_final: 0.3513 (mtm180) REVERT: D 824 GLU cc_start: 0.6050 (pt0) cc_final: 0.5629 (mt-10) REVERT: D 830 GLU cc_start: 0.6168 (mp0) cc_final: 0.5809 (mp0) REVERT: D 936 TYR cc_start: 0.4854 (OUTLIER) cc_final: 0.4200 (t80) REVERT: D 971 TYR cc_start: 0.2813 (OUTLIER) cc_final: -0.1055 (p90) REVERT: D 1320 ASP cc_start: 0.5107 (t0) cc_final: 0.4758 (t0) REVERT: D 1831 TRP cc_start: 0.5945 (t-100) cc_final: 0.5624 (t-100) REVERT: D 1909 LEU cc_start: 0.6505 (mm) cc_final: 0.6187 (tp) outliers start: 26 outliers final: 16 residues processed: 95 average time/residue: 0.0931 time to fit residues: 11.8020 Evaluate side-chains 96 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 913 LYS Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1317 MET Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1757 TYR Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 982 ASN D1727 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.170975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.155622 restraints weight = 16635.895| |-----------------------------------------------------------------------------| r_work (start): 0.4656 rms_B_bonded: 3.17 r_work: 0.4538 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5622 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7053 Z= 0.189 Angle : 0.733 7.062 9814 Z= 0.376 Chirality : 0.043 0.164 1138 Planarity : 0.006 0.064 1053 Dihedral : 18.452 163.935 1599 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.92 % Allowed : 24.00 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.31), residues: 690 helix: -0.30 (0.29), residues: 282 sheet: -3.59 (0.82), residues: 25 loop : -1.82 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 944 TYR 0.021 0.002 TYR D1701 PHE 0.023 0.002 PHE D1332 TRP 0.025 0.004 TRP D1048 HIS 0.008 0.001 HIS D1041 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 7053) covalent geometry : angle 0.73297 ( 9814) hydrogen bonds : bond 0.06265 ( 272) hydrogen bonds : angle 5.96929 ( 730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 936 TYR cc_start: 0.4913 (OUTLIER) cc_final: 0.3924 (t80) REVERT: D 1320 ASP cc_start: 0.5279 (t0) cc_final: 0.4960 (t0) REVERT: D 1691 SER cc_start: 0.6206 (p) cc_final: 0.5480 (t) REVERT: D 1722 GLU cc_start: 0.4816 (OUTLIER) cc_final: 0.3554 (mp0) REVERT: D 1831 TRP cc_start: 0.5924 (t-100) cc_final: 0.5562 (t-100) REVERT: D 1909 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6317 (tp) outliers start: 37 outliers final: 22 residues processed: 109 average time/residue: 0.1004 time to fit residues: 14.1967 Evaluate side-chains 106 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 913 LYS Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1020 ARG Chi-restraints excluded: chain D residue 1062 HIS Chi-restraints excluded: chain D residue 1314 ARG Chi-restraints excluded: chain D residue 1317 MET Chi-restraints excluded: chain D residue 1357 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1662 LEU Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1767 HIS Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1893 VAL Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.172542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.157945 restraints weight = 17740.539| |-----------------------------------------------------------------------------| r_work (start): 0.4685 rms_B_bonded: 3.11 r_work: 0.4572 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 7053 Z= 0.163 Angle : 0.728 7.976 9814 Z= 0.369 Chirality : 0.043 0.304 1138 Planarity : 0.006 0.066 1053 Dihedral : 18.450 163.481 1599 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.83 % Favored : 92.03 % Rotamer: Outliers : 4.48 % Allowed : 26.40 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.31), residues: 690 helix: -0.10 (0.30), residues: 284 sheet: -3.66 (0.77), residues: 25 loop : -1.78 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 789 TYR 0.024 0.002 TYR D1820 PHE 0.021 0.002 PHE D1332 TRP 0.023 0.003 TRP D1048 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7053) covalent geometry : angle 0.72756 ( 9814) hydrogen bonds : bond 0.06188 ( 272) hydrogen bonds : angle 5.89522 ( 730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 830 GLU cc_start: 0.6318 (mp0) cc_final: 0.6001 (mp0) REVERT: D 1320 ASP cc_start: 0.5233 (t0) cc_final: 0.4899 (t0) REVERT: D 1691 SER cc_start: 0.6397 (p) cc_final: 0.5610 (t) REVERT: D 1722 GLU cc_start: 0.4730 (OUTLIER) cc_final: 0.3560 (mp0) REVERT: D 1831 TRP cc_start: 0.5924 (t-100) cc_final: 0.5595 (t-100) REVERT: D 1909 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6254 (tp) outliers start: 28 outliers final: 22 residues processed: 100 average time/residue: 0.1030 time to fit residues: 13.3160 Evaluate side-chains 107 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1020 ARG Chi-restraints excluded: chain D residue 1314 ARG Chi-restraints excluded: chain D residue 1317 MET Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1357 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1662 LEU Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1757 TYR Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1857 LEU Chi-restraints excluded: chain D residue 1893 VAL Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.173212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.158585 restraints weight = 17863.720| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 3.08 r_work: 0.4574 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5506 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 7053 Z= 0.161 Angle : 0.736 11.011 9814 Z= 0.375 Chirality : 0.043 0.295 1138 Planarity : 0.006 0.058 1053 Dihedral : 18.446 162.799 1599 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.97 % Favored : 91.88 % Rotamer: Outliers : 4.48 % Allowed : 26.56 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.31), residues: 690 helix: 0.07 (0.30), residues: 283 sheet: -3.96 (0.58), residues: 34 loop : -1.87 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 996 TYR 0.036 0.002 TYR D 976 PHE 0.030 0.002 PHE D1758 TRP 0.014 0.002 TRP D1048 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7053) covalent geometry : angle 0.73637 ( 9814) hydrogen bonds : bond 0.06068 ( 272) hydrogen bonds : angle 5.84235 ( 730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.4313 (OUTLIER) cc_final: 0.3978 (mtp180) REVERT: D 830 GLU cc_start: 0.6171 (mp0) cc_final: 0.5892 (mp0) REVERT: D 936 TYR cc_start: 0.4890 (OUTLIER) cc_final: 0.4467 (t80) REVERT: D 1020 ARG cc_start: 0.4350 (OUTLIER) cc_final: 0.3800 (ptm-80) REVERT: D 1030 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7032 (mtpt) REVERT: D 1320 ASP cc_start: 0.5307 (t0) cc_final: 0.4976 (t0) REVERT: D 1691 SER cc_start: 0.6314 (p) cc_final: 0.5789 (p) REVERT: D 1722 GLU cc_start: 0.4710 (OUTLIER) cc_final: 0.3598 (mp0) REVERT: D 1831 TRP cc_start: 0.5882 (t-100) cc_final: 0.5558 (t-100) REVERT: D 1909 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6199 (tp) outliers start: 28 outliers final: 19 residues processed: 101 average time/residue: 0.1039 time to fit residues: 13.4218 Evaluate side-chains 106 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1020 ARG Chi-restraints excluded: chain D residue 1314 ARG Chi-restraints excluded: chain D residue 1317 MET Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1357 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1857 LEU Chi-restraints excluded: chain D residue 1893 VAL Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 30.0000 chunk 16 optimal weight: 0.0570 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.0470 chunk 55 optimal weight: 0.4980 chunk 29 optimal weight: 0.0000 chunk 24 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 overall best weight: 0.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 985 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.176697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.162895 restraints weight = 17504.272| |-----------------------------------------------------------------------------| r_work (start): 0.4766 rms_B_bonded: 2.93 r_work: 0.4656 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7053 Z= 0.141 Angle : 0.722 10.643 9814 Z= 0.364 Chirality : 0.042 0.191 1138 Planarity : 0.006 0.055 1053 Dihedral : 18.439 162.706 1599 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.97 % Favored : 91.88 % Rotamer: Outliers : 4.64 % Allowed : 26.40 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.31), residues: 690 helix: 0.25 (0.31), residues: 281 sheet: -3.79 (0.65), residues: 35 loop : -1.84 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 996 TYR 0.019 0.002 TYR D1820 PHE 0.021 0.002 PHE D1758 TRP 0.012 0.002 TRP D1048 HIS 0.007 0.001 HIS D1062 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7053) covalent geometry : angle 0.72233 ( 9814) hydrogen bonds : bond 0.06038 ( 272) hydrogen bonds : angle 5.73628 ( 730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.4597 (OUTLIER) cc_final: 0.4182 (mtp180) REVERT: D 971 TYR cc_start: 0.2485 (OUTLIER) cc_final: -0.1060 (p90) REVERT: D 1020 ARG cc_start: 0.4111 (OUTLIER) cc_final: 0.3715 (ptm-80) REVERT: D 1030 LYS cc_start: 0.7401 (mmtt) cc_final: 0.6916 (mtpt) REVERT: D 1320 ASP cc_start: 0.4700 (t0) cc_final: 0.4414 (t0) REVERT: D 1722 GLU cc_start: 0.4886 (OUTLIER) cc_final: 0.4648 (mt-10) REVERT: D 1831 TRP cc_start: 0.5920 (t-100) cc_final: 0.5638 (t-100) REVERT: D 1909 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.6117 (tp) outliers start: 29 outliers final: 18 residues processed: 100 average time/residue: 0.1065 time to fit residues: 13.6122 Evaluate side-chains 98 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1020 ARG Chi-restraints excluded: chain D residue 1314 ARG Chi-restraints excluded: chain D residue 1317 MET Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1357 TYR Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1757 TYR Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1839 ARG Chi-restraints excluded: chain D residue 1857 LEU Chi-restraints excluded: chain D residue 1893 VAL Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0086 > 50: distance: 74 - 78: 35.544 distance: 78 - 79: 48.513 distance: 79 - 82: 41.989 distance: 80 - 81: 27.893 distance: 80 - 84: 10.546 distance: 81 - 109: 41.380 distance: 82 - 83: 27.202 distance: 84 - 85: 39.722 distance: 84 - 90: 55.907 distance: 85 - 86: 39.501 distance: 85 - 88: 43.397 distance: 86 - 87: 43.857 distance: 86 - 91: 16.628 distance: 88 - 89: 25.832 distance: 89 - 90: 41.208 distance: 91 - 92: 15.683 distance: 92 - 93: 43.223 distance: 93 - 94: 44.103 distance: 93 - 98: 18.079 distance: 95 - 96: 55.135 distance: 95 - 97: 52.303 distance: 98 - 99: 57.839 distance: 99 - 100: 24.620 distance: 99 - 102: 44.199 distance: 100 - 101: 57.020 distance: 100 - 109: 56.504 distance: 101 - 134: 20.397 distance: 102 - 103: 63.720 distance: 103 - 104: 42.225 distance: 104 - 105: 56.024 distance: 105 - 106: 41.072 distance: 106 - 107: 41.202 distance: 106 - 108: 41.961 distance: 109 - 110: 40.938 distance: 110 - 111: 50.661 distance: 110 - 113: 57.784 distance: 111 - 112: 40.269 distance: 111 - 118: 69.988 distance: 112 - 143: 39.018 distance: 113 - 114: 55.877 distance: 114 - 115: 39.189 distance: 115 - 116: 41.374 distance: 115 - 117: 62.783 distance: 118 - 119: 17.181 distance: 119 - 120: 34.874 distance: 119 - 122: 59.734 distance: 120 - 121: 11.604 distance: 120 - 126: 13.574 distance: 121 - 151: 41.111 distance: 122 - 123: 5.154 distance: 123 - 124: 63.219 distance: 126 - 127: 42.126 distance: 127 - 128: 63.713 distance: 127 - 130: 48.671 distance: 128 - 129: 56.769 distance: 128 - 134: 43.872 distance: 130 - 131: 30.862 distance: 131 - 132: 24.133 distance: 131 - 133: 30.516 distance: 134 - 135: 43.417 distance: 135 - 136: 55.935 distance: 135 - 138: 46.365 distance: 136 - 137: 39.896 distance: 136 - 143: 56.353 distance: 138 - 139: 37.838 distance: 139 - 140: 33.457 distance: 140 - 141: 31.060 distance: 140 - 142: 17.810 distance: 143 - 144: 39.504 distance: 144 - 145: 55.196 distance: 144 - 147: 26.607 distance: 145 - 146: 56.440 distance: 147 - 148: 44.034 distance: 148 - 149: 41.256 distance: 149 - 150: 10.406 distance: 152 - 153: 55.279 distance: 152 - 155: 55.519 distance: 153 - 160: 32.775 distance: 155 - 156: 41.006 distance: 156 - 157: 39.986 distance: 157 - 158: 39.985 distance: 157 - 159: 23.307